I think it is more likely you have the save template producing the same file name for multiple books. My guess would be the save template looks something like one of the following:
Code:
{author_sort}/{authors}
{author_sort}/{series} - {authors}
There isn't enough in either of those to uniquely identity a book. The first one means you will only have one book by an author on the device, the second, only one book per series for the author.
My save template is:
Code:
{author_sort}/{title} - {authors}
That is unique enough unless you allow duplicates in your calibre library or have multiple editions or something like that.
The save template is in the configuration of the driver. You can access this through the Plugins section of the preferences, or by right-clicking on the device button when the device is connected.